Kinetic Monte Carlo Study Research Articles

Quantifying STM-tip induced directed hopping of Sb2 dimers on Si(001): A kinetic Monte Carlo study

In this study, kinetic Monte Carlo simulations of a lattice gas model were performed to investigate the experimentally observed enhanced directed diffusion of Sb2 ad-dimers on Si(001) during asymmetric scanning—one that uses invasive and noninvasive scanning tunneling microscope (STM) settings for leftward and rightward scanning, respectively. The authors model the invasive scanning by postulating an attractive interaction between the STM tip and the adsorbates. This is done by lowering (raising) the activation barrier by an adjustable energy difference ΔE for hopping of Sb2 dimers toward (away from) the STM tip site. Effectively, ΔE is a measure of the severity of the STM tip's impact on surface kinetics. Additionally, they explore the effect of varying ΔE on the activation barrier for hopping of Sb2 dimers orthogonal to the Si dimer rows by setting its value to 0.1–0.4 eV. Experimentally determined to be 1.2 eV, the authors found that for very small ΔE (ΔE < 0.1 eV) the activation barrier could be underestimated by no more than 0.03 eV, and as much as 0.13 eV for large ΔE (ΔE = 0.4 eV). Next, they ask if this model could induce asymmetry in the hopping frequency under asymmetric scanning, that is, STM runs in the invasive mode when moving from right to left, and noninvasive mode in the opposite direction. The authors found that indeed there is a net movement of Sb2 dimers from right to left, or along the direction of the invasive scan. Moreover, they found that this directed motion becomes slightly more pronounced as the scanning speed decreases. These twin observations were explained by noting the asymmetry in the occupation probability of the sites immediately to the left and right of the STM tip—the site trailing the tip, or the site to its right, is more likely to be occupied compared than the one leading it. In this sense, according to their model, the STM tip gently drags the adsorbates it comes in contact with but falls short of precise, active manipulation even for large ΔE (ΔE = 0.4 eV).

DFT and Kinetic Monte Carlo Study of TMS-Substituted Ruthenium Vinyl Carbenes: Key Intermediates for Stereoselective Cyclizations

Mechanistic pathways for the cyclization of 1,5-alkynylacetal with N2CHTMS in the presence of Cp- and Cp*RuCl(cod) to afford (Z)- and (E)-(trimethylsilyl)vinyl spiroacetals have been calculated. Calculations show the presence of three conformers in equilibrium for the initially formed ruthenium carbenes. Differences in the stabilities and reactivities of the conformers, depending on the use of a Cp or Cp* ruthenium catalyst, are responsible for the favorable active reaction pathways in each case, even though the geometry of the resulting product is the same regardless of the catalyst used. Kinetic Monte Carlo (KMC) simulations with rate coefficients, including tunneling probabilities for the hydride transfer step, were used to model the evolution of reactants, intermediates, and products for all calculated pathways. It was shown that one path is almost exclusively active for each catalyst. Finally, the energetic span model of Kozuch and Shaik was used to calculate the energetic span (δE), the TOF-determining transition state (TDTS), the TOF-determining intermediate (TDI), and the TOF value for each of the feasible mechanistic pathways.

Kinetic Monte Carlo study of structural proton diffusion along a one-dimensional path

We study the structural diffusion coefficient of protons in a chain-like system by the means of KMC simulations. To perform specific calculations, we adopted parameter values in our model that correspond to the benzimidazole crystal. As we have shown, the structural diffusion follows the Arrhenius-like thermal dependence with an effective activation energy of 2.01 eV.

A kinetic Monte Carlo study of defect assisted transport in silicon heterojunction solar cells

AbstractThe device performance of an amorphous silicon (a‐Si)/crystalline silicon (c‐Si) solar cell depends strongly on the interfacial transport properties of the device. The energy of the photogenerated carriers at the barrier strongly depends on the strength of the inversion at the heterointerface and their collection requires interaction with the defects present in the intrinsic amorphous silicon buffer layer. In this work we present a theoretical model to study the defect assisted transport of photogenerated carriers through the intrinsic amorphous silicon barrier. We implement the kinetic Monte Carlo (KMC) method which allows us to simulate the interaction of discrete carriers with discrete defects. This method allows us to study defect transport which takes place on a time scale which is too long for traditional ensemble Monte Carlo's to analyze. We analyze the injection and extraction of carriers via defects by calculating transition rates, i.e. probability of transition to defect states within the intrinsic amorphous silicon barrier. The KMC results allow us to quantitatively study the properties of the heterointerface barrier in terms of how it affects transport. (© 2015 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)

Large-scale epitaxial growth kinetics of graphene: A kinetic Monte Carlo study.

Epitaxial growth via chemical vapor deposition is considered to be the most promising way towards synthesizing large area graphene with high quality. However, it remains a big theoretical challenge to reveal growth kinetics with atomically energetic and large-scale spatial information included. Here, we propose a minimal kinetic Monte Carlo model to address such an issue on an active catalyst surface with graphene/substrate lattice mismatch, which facilitates us to perform large scale simulations of the growth kinetics over two dimensional surface with growth fronts of complex shapes. A geometry-determined large-scale growth mechanism is revealed, where the rate-dominating event is found to be C1-attachment for concave growth-front segments and C5-attachment for others. This growth mechanism leads to an interesting time-resolved growth behavior which is well consistent with that observed in a recent scanning tunneling microscopy experiment.

Effects of pressure, temperature and atomic exchanges on phase separation dynamics in Au/Ni(111) surface alloy: Kinetic Monte Carlo study

Instability of the Au/Ni(111) surface alloy is studied in different CO gas pressure, p, and temperature limits using kinetic Monte Carlo simulations. We analyze the reaction front dynamics and formation of Au clusters using the model which takes into account surface adatom pair and three-body interactions, CO adsorption and desorption, catalytic carbonyl formation reaction, Au and Ni adatom diffusion and their concerted exchange. Variation of interaction parameters allows us to identify three possible reaction front propagation limits with different pressure dependencies: (i) slow channel-like flow in agreement with experimental data [1] (step flow rate, R, increases with p), (ii) intermediate regime (weak p–dependence), and (iii) fast homogeneous flow (R decreases with p). We find that only Au–Ni exchange, contrary to both Ni–CO and Au–CO exchanges, significantly reduces the number of screened Ni atoms inside the Au clusters and stimulates the occurrence of Ni-free Au clusters. The size of Au islands depends on both pressure and temperature. At a fixed temperature it decreases with pressure due to an increased step flow rate. In the high temperature limit, despite the step flow rate exponential increase with temperature, the cluster size increases due to an enhanced Au mobility.

Magnetization dynamics of mixed Co–Au chains on Cu(110) substrate: Combined ab initio and kinetic Monte Carlo study**Project supported by the Russian Foundation of Basic Researches.

We present an investigation of the one-dimensional ferromagnetism in Au–Co nanowires deposited on the Cu(110) surface. By using the density functional theory, the influence of the nonmagnetic copper substrate Cu(110) on the magnetic properties of the bimetallic Au–Co nanowires is studied. The results show the emergence of magnetic anisotropy in the supported Au–Co nanowires. The magnetic anisotropy energy has the same order of magnitude as the exchange interaction energy between Co atoms in the wire. Our electronic structure calculation reveals the emergence of new hybridized bands between Au and Co atoms and surface Cu atoms. The Curie temperature of the Au–Co wires is calculated by means of kinetic Monte Carlo simulation. The strong size effect of the Curie temperature is demonstrated.

Size calibration of epitaxial islands via a two-step growth protocol: Kinetic Monte Carlo and effective-medium theory study

Abstract The kinetic Monte Carlo technique has been used to simulate irreversible growth of epitaxial islands in two consecutive steps. At the first step a small quantity of adatoms was simultaneously deposited at the surface at random positions and the atoms freely diffuse until nucleating new islands or until being caught by the earlier nucleated ones. It was found that the distribution of the Voronoi cell (VC) areas around the island centers could be accurately described by the Gaussian distribution (GD) which was narrower than the GD describing the VCs of randomly distributed nucleation centers. Thus, our simulations provide an alternative explanation of the narrowing that was observed experimentally and attributed to elastic forces. At the second step the surface was exposed to an atomic deposition flux that was chosen to be small enough for the nucleation of new islands was strongly suppressed and the growth was dominated by the aggregation of deposited atoms into existing islands. At this step the island size distributions (ISDs) obtained could be also well described by the GD only more peaked than the corresponding VC area distributions. The narrowing has been explained in the framework of an effective medium theory. In several cases the simulated VC area distributions and ISDs semi-quantitatively agreed with those observed experimentally. Furthermore, the two-step growth made the island diameter distributions much more symmetric than those obtained under the conventional irreversible growth setup. It is suggested that this technique may provide a method of controlled growth of the island ensembles with narrow and symmetric size distributions in practically any system: homo- or heteroepitaxial.

Non-Arrhenius temperature dependence of the island density of one-dimensional Al chains on Si(100): A kinetic Monte Carlo study

Classical nucleation theory predicts that the evolution of mean island density with temperature during growth in one-dimensional systems obeys the Arrhenius relation. In this study, kinetic Monte Carlo simulations of a suitable atomistic lattice-gas model were performed to investigate the experimentally observed non-Arrhenius scaling behavior of island density in the case of one-dimensional Al islands grown on Si(100). Previously, it was proposed that adatom desorption resulted in a transition temperature signaling the departure from classical predictions. Here, the authors demonstrate that desorption above the transition temperature is not possible. Instead, the authors posit that the existence of a transition temperature is due to a combination of factors such as reversibility of island growth, presence of C-defects, adatom diffusion rates, as well as detachment rates at island ends. In addition, the authors show that the anomalous non-Arrhenius behavior vanishes when adatom binds irreversibly with C-defects as observed in In on Si(100) studies.

First-principles-based kinetic Monte Carlo studies of diffusion of hydrogen in Ni–Al and Ni–Fe binary alloys

The diffusion of dilute hydrogen in fcc Ni–Al and Ni–Fe binary alloys was examined using kinetic Monte Carlo method with input kinetic parameters obtained from first-principles density functional theory. The simulation involves the implementation of computationally efficient energy barrier model that describes the configuration dependence of the hydrogen hopping. The predicted hydrogen diffusion coefficients in Ni and Ni89.4Fe10.6 are compared well with the available experimental data. In Ni–Al, the model predicts lower hydrogen diffusivity compared to that in Ni. Overall, diffusion prefactors and the effective activation energies of H in Ni–Fe and Ni–Al are concentration dependent of the alloying element. The changes in their values are the results of the short-range order (nearest-neighbor) effect on the interstitial diffusion of hydrogen in fcc Ni-based alloys.

A Kinetic Monte Carlo Study of Fullerene Adsorption within a Pc-PBBA Covalent Organic Framework and Implications for Electron Transport.

Two-dimensional covalent organic frameworks (COFs), with their predictable assembly into ordered porous crystalline materials, tunable composition, and high charge carrier mobility, offer the possibility of creating ordered bulk heterojunction solar cells given a suitable electron-transporting material to fill the pores. The photoconductive (hole-transporting) properties of many COFs have been reported, including the recent creation of a TT-COF/PCBM solar cell by Dogru et al. Although a prototype device has been fabricated, its poor solar efficiency suggests a potential issue with electron transport caused by the interior packing of the fullerenes. Such packing information is absent and cannot be obtained experimentally. In this paper, we use Kinetic Monte Carlo (KMC) simulations to understand the dominant pore-filling mechanisms and packing configurations of C60 molecules in a Pc-PBBA COF that are similar to the COF fabricated experimentally. The KMC simulations thus offer more realistic filling conditions than our previously used Monte Carlo (MC) techniques. We found persistently large separation distances between C60 molecules that are absent in the more tractable MC simulations and which are likely to hinder electron transport significantly. We attribute the looser fullerene packing to the existence of stable motifs with pairwise distances that are mismatched with the underlying adsorption lattice of the COF. We conclude that larger pore COFs may be necessary to optimize electron transport and hence produce higher efficiency devices.

Stability and mobility of small vacancy–solute complexes in Fe–MnNi and dilute Fe–X alloys: A kinetic Monte Carlo study

Manganese and nickel solute atoms in irradiated ferritic steels play a major role in the nanostructural evolution of reactor pressure vessels (RPV), as they are responsible for the formation of embrittling nanofeatures even in the absence of copper. The stability and mobility of small vacancy–solute clusters is here studied with an atomistic kinetic Monte Carlo approach based on ab initio calculations, in order to investigate the influence of Mn and Ni on the early life of small radiation-induced vacancy clusters, and to provide the necessary parameters for advanced object kinetic Monte Carlo simulations of the RPV long-term nanostructural evolution. Migration barriers are obtained by direct ab initio calculations or through a binding energy model based on ab initio data. Our results show a clear immobilizing and stabilizing effect on vacancy clusters as the solute content is increased, whereas the only evident difference between the two solute species is a somewhat longer elongation of the cluster mean free path in the presence of a few Mn atoms.

Kinetic Monte Carlo Study of the Type 1/Type 2 Choice in Apoptosis Elucidates Selective Killing of Cancer Cells under Death Ligand Induction

Death ligand mediated apoptotic activation is a mode of programmed cell death that is widely used in cellular and physiological situations. Interest in studying death ligand induced apoptosis has increased due to the promising role of recombinant soluble forms of death ligands (mainly recombinant TRAIL) in anti-cancer therapy. A clear elucidation of how death ligands activate the type 1 and type 2 apoptotic pathways in healthy and cancer cells may help develop better chemotherapeutic strategies. In this work, we use kinetic Monte Carlo simulations to address the problem of type 1/ type 2 choice in death ligand mediated apoptosis of cancer cells. Our study provides insights into the activation of membrane proximal death module that results from complex interplay between death and decoy receptors. Relative abundance of death and decoy receptors was shown to be a key parameter for activation of the initiator caspases in the membrane module. Increased concentration of death ligands frequently increased the type 1 activation fraction in cancer cells, and, in certain cases changes the signaling phenotype from type 2 to type 1. Results of this study also indicate that inherent differences between cancer and healthy cells, such as in the membrane module, may allow robust activation of cancer cell apoptosis by death ligand induction. At the same time, large cell-to-cell variability through the type 2 pathway was shown to provide protection for healthy cells. Such elucidation of selective activation of apoptosis in cancer cells addresses a key question in cancer biology and cancer therapy.

Kinetic Monte Carlo Study of the Sensitivity of OLED Efficiency and Lifetime to Materials Parameters

The performance of organic light‐emitting diodes (OLEDs) is determined by a complex interplay of the optoelectronic processes in the active layer stack. In order to enable simulation‐assisted layer stack development, a three‐dimensional kinetic Monte Carlo OLED simulation method which includes the charge transport and all excitonic processes is developed. In this paper, the results are presented of simulations including degradation processes in idealized but realizable phosphorescent OLEDs. Degradation is treated as a result of the conversion of emitter molecules to non‐emissive sites upon a triplet‐polaron quenching (TPQ) process. Under the assumptions made, TPQ provides the dominant contribution to the roll‐off. There is therefore a strong relationship between the roll‐off and the lifetime. This is quantified using a “uniform density model”, within which the charge carrier and exciton densities are assumed to be uniform across the emissive layer. The simulations give rise to design rules regarding the energy levels, and are used to study the sensitivity of the roll‐off and lifetime to various other materials parameters, including the mobility, the phosphorescent dye concentration, the triplet exciton emissive lifetime and binding energy, and the type of TPQ process.

Theoretical study of the ammonia nitridation rate on an Fe (100) surface: a combined density functional theory and kinetic Monte Carlo study.

Ammonia (NH3) nitridation on an Fe surface was studied by combining density functional theory (DFT) and kinetic Monte Carlo (kMC) calculations. A DFT calculation was performed to obtain the energy barriers (Eb) of the relevant elementary processes. The full mechanism of the exact reaction path was divided into five steps (adsorption, dissociation, surface migration, penetration, and diffusion) on an Fe (100) surface pre-covered with nitrogen. The energy barrier (Eb) depended on the N surface coverage. The DFT results were subsequently employed as a database for the kMC simulations. We then evaluated the NH3 nitridation rate on the N pre-covered Fe surface. To determine the conditions necessary for a rapid NH3 nitridation rate, the eight reaction events were considered in the kMC simulations: adsorption, desorption, dissociation, reverse dissociation, surface migration, penetration, reverse penetration, and diffusion. This study provides a real-time-scale simulation of NH3 nitridation influenced by nitrogen surface coverage that allowed us to theoretically determine a nitrogen coverage (0.56 ML) suitable for rapid NH3 nitridation. In this way, we were able to reveal the coverage dependence of the nitridation reaction using the combined DFT and kMC simulations.

Kinetic Monte Carlo Studies of Enhanced Chemical Reactions on Nanoporous Electrodes

Kinetic Monte Carlo studies of enhanced chemical reactions on nanoporous electrodesNanoporous electrodes have the effect of enhancing kinetically-limited electrochemical reactions due to the enlargement of electrode surface area. It has recently been reported that the confinement effect of reactants in the pores plays an important role for the enhancement of the reactions[1, 2]. By using these catalytic effect of nanoporous electrodes, the application to nonenzymic sensor (ex. glucose) has been explored[3]. The purpose of the present work is to study the effects of nanoporous electrodes on the enhanced chemical reactions on an atomic length scale by the kinetic Monte Carlo (KMC) simulation. We focus our attention on the confinement effect of reactants as well as the enlargement of the electrode area. We have developed a combination of KMC and grand canonical Monte Carlo (GCMC) for the multiscale simulation of the reactions and the mass transport in solution.We have performed a series of KMC-GCMC simulations to study the correlation between the porous structures (cylindrical, random) and the enhancement of the reactions. The simulation system is a three-dimensional square lattice consisting of electrode, solution and replenishing region. Figure-1 is a schematic diagram of this system. Reactant particles are distributed in solution and their diffusion is simulated by random walk. The upper part of the solution is a replenishing layer to supply the reactant particles when the concentration becomes low as a result of the surface reactions. We consider a simple electrode reaction. It is assumed that reactants are removed on the electrode with a given rate constant. We consider two types of pore structures; cylindrical pore and random pore. The diffusion and reaction of the particles are simulated by KMC method. The replenishing layer is simulated by GCMC method.We first confirmed that nanoporous electrodes enhance slow reactions compared to flat electrodes. The influence of the pore structures on the reaction mechanism is studied in detail. We also study the reaction of the mixture of slow and fast reactant particles as an application to the sensors.

A kinetic Monte Carlo study of coarsening resistance of novel core/shell precipitates

A novel approach towards the design of coarsening-resistant nanoprecipitates in structural alloys was investigated by kinetic Monte Carlo (KMC) simulation. The approach is motivated by recent experimental results in Cu–Nb–W alloys showing that room temperature ion irradiation resulted in W nanoprecipitation, leading to exceptional stability of W-rich-core/Nb-rich-shell nanoprecipitates formed following thermal annealing (Zhang et al., 2013 [11]). Here, image simulations of atomically resolved scanning transmission electron microscopy are performed to establish that these W nanoprecipitates are highly ramified. Thermal precipitate coarsening in an A–B–C ternary alloy similar to Cu–Nb–W is then studied by KMC simulations, where the highly immiscible and refractory C solute atoms are initially distributed into fractal nanoprecipitates, or cores, which become coated by a shell of B atoms during elevated temperature annealing. Compared with nanoprecipitates generated by compact C cores, the ramified nanoprecipitates result in exceptionally high trapping efficiency of B solute atoms during thermal coarsening, and the efficiency increases with the cluster size. The KMC results are analyzed and rationalized by noting that, owing to the Gibbs–Thomson effect, when the curvatures of the shell of the precipitates are zero or negative, the microstructure is coarsening-resistant. Such morphology can be realized by facets, or by dynamic balance within positive, negative and zero curvatures.

Impact of STM tip on coarsening of In atomic chains on Si(100): A kinetic Monte Carlo study

Using a Kinetic Monte Carlo approach, we investigate the potential influence of STM tip on nucleation and subsequent growth of single-atom wide In chains on Si(100) during room-temperature deposition. Specifically, we examine the effect of repeated scanning on the stability of odd-size chains, as well as coarsening of chains in the post-deposition regime. In our simulations, the effects of the strong field developed between the STM tip and the positively charged In adsorbates when the sample is positively (negatively) biased are modeled by slightly lowering (raising) the activation barriers of adatoms directly underneath the tip. Evidence of stochastic ripening – a coarsening mechanism relying on a series of adatom exchanges between adjacent islands in one-dimensional systems and not driven by a difference in the chemical potential – will be presented. Finally, we will show that coarsening may be disrupted by STM tip effects.

Oxide ion and proton transport in Gd-doped barium cerate: a combined first-principles and kinetic Monte Carlo study

Oxide ion and proton transport properties in the fuel cell electrolyte Gd-doped BaCeO3 are investigated by first-principles density-functional calculations and kinetic Monte Carlo simulations. Behind the apparent complexity of the energy landscape (related to the low-symmetry of the system), general tendencies governing the energy barriers can be extracted. In particular, the set of barriers is tested with respect to the Bell–Evans–Polanyi (BEP) principle that relates the activation energy Ea of a series of similar chemical reactions to their reaction enthalpies ΔH. This rule is found poorly satisfied in the case of oxide ion migration, but much better satisfied for proton hopping mechanisms. Protonic reorientations, by contrast, do not obey the BEP rule. Kinetic Monte Carlo simulations give insight into the macroscopic transport properties. We observe that dopants act as traps for oxygen vacancies and slow down their motion, whereas their effect on the protonic diffusion coefficient is more complex. This is related to the fact that a two-state picture roughly applies to the oxygen vacancy energy landscape, while it does not apply to the protonic one. Oxide ion migration exhibits strong anisotropy, the motion of the oxygen vacancies being favored in the equatorial planes, while protonic diffusion is found more isotropic.

Are hot charge transfer states the primary cause of efficient free-charge generation in polymer:fullerene organic photovoltaic devices? A kinetic Monte Carlo study.

Kinetic Monte Carlo simulations are used to examine the effect of high-energy, 'hot' delocalised charge transfer (HCT) states for donor:acceptor and mixed:aggregate blends, the latter relating to polymer:fullerene photovoltaic devices. Increased fullerene aggregation is shown to enhance charge generation and short-circuit device current - largely due to the increased production of HCT states at the aggregate interface. However, the instances where HCT states are predicted to give internal quantum efficiencies in the region of 50% do not correspond to HCT delocalisation or electron mobility measured in experiments. These data therefore suggest that HCT states are not the primary cause of high quantum efficiencies in some polymer:fullerene OPVs. Instead it is argued that HCT states are responsible for the fast charge generation seen in spectroscopy, but that regional variation in energy levels are the cause of long-term, efficient free-charge generation.